Dear Branko, I have just seen your comment that you have an issue with XPS, which is my BioC package. However, you have never contacted me at <[email protected]> nor have sent a mail to the BioC mailing list. I would really appreciate that you contact me first before making such a statement.
Regarding your problem with HuGene-1_0-st-v1.na30.hg19.probeset._csv, (which could be the reason of your problem with xps), Affymetrix had included probesets in this annotation file which were not included in the corresponding *.PGF file. For this reason I have contacted Affymetrix DevNet and asked them to remove the extra probesets, which they kindly did resulting in file HuGene-1_0-st- v1.na30.1.hg19.probeset._csv. Best regards Christian On Jan 28, 4:58 pm, branko <[email protected]> wrote: > Hi all, > > First to thank you Mark , Henrik for nice tool and also all others > for informative mailing list. > This is my first email so hopefully not so many dummy questions. > > I found this thread as it is linked to my first 2 questions: > Month ago I did some basic analysis with 300 chips where your tool > got very handy. And I'm starting again to analyze things ... > (Btw. I found about Aroma on BioC list as I had issue with XPS > package that I couldn’t resolve . I would like to have them both > working so Xps will come on board eventually.) > > Now regarding this tread. > 1) When I compared HuGene-1_0-st-v1.na30.hg19.probeset._csv. with > the Aroma CDF file there are > 33257 PSets in csv while Aroma has 33252 so 4 different. So > maybe the CDF update is needed in Aroma? > I also just saw some more recent update on Affymetrix to “na30.1” > and I see I have used “na30” csv file. > > Following seems weird , many ProbeSets have no gene symbol > annotation in “main“ category : > > tr <- read.csv ( "HuGene-1_0-st-v1.na30.hg19.transcript.csv" , > stringsAsFactors =F ,comment.char="#") > > sum(tr$gene_assignment=="---" & tr$category=="main") #6711 > sum(tr$unigene=="---" & tr$category=="main") #7376 > sum(tr$swissprot=="---" & tr$category=="main") # 8021 > > Affy 33257 Probesets are classified as: > TYPE TOTAL > control->affx 57 > control->bgp->antigenomic 45 > main 28829 > normgene->exon 1195 > normgene->intron 2904 > rescue->FLmRNA->unmapped 227 > > Do you maybe know why are there so many e.g above 6711 without > gene_assignment ? > > 2) One more related to 1st Q : How to run normalization only on > ProbeSet classified as “main” ? ( Affymetrix csv file says this > class has 28829 > Psets in main class) Idea is of course to minimize > normalization bias of non-main class Psets. > > 3) Few questions regarding Quality checks and basic data > manipulations in Aroma: > I would like to give meaningful labels to the Arrays in the e.g. > box-plots (instead of CEL file names, as said i have 300) . > How can I do that? > Also how can I sort them ? > I ask this silly questions because Using R commands like str() > doesn’t show me the > object fields etc. so I can’t use standard R matrix commands, > also help (“some Aroma command” ) doesn’t show enough information. > Sometimes it gives empty help page. > I could not find pdf manual in Aroma installed libraries nor in > the Google group. I see only html file showing me all the functions & > classes. > Is there easier way to look for functions than main html pages ? > Code of functions are not visible by just typing func.name() , I > guess I can always get source code and search but there is likely easy > way to do it. > > It is visible that Aroma uses different classes than > BioConductor. I assume there is a good reason for that, but maybe you > can give some link with explanation? > > Oh and thank you for putting clean instructions for basic > preprocessing steps to get Expression matrix out for further > analysis. > > One example of my attempt to searching things : > cs <- AffymetrixCelSet$byName(dataSet, cdf=cdf) > print(cs) > str(cs) > #Classes 'AffymetrixCelSet', 'AffymetrixFileSet', > 'AromaPlatformInterface', 'AromaMicroarrayDataSet', > 'GenericDataFileSet', 'FullNameInterface', 'Object' atomic [1:1] NA > …. > ?classname put me on some track. > > So I looked a bit and I saw GenericDataFileSet class provides > function > getFullNames() and it does give me the my CEL filenames (btw. > help on ?getFullNames gives me no help .) > setNames() point to basic library… but before going deeper and > making some mess I hope you > can give me answer on above questions or some links ? > > 4) Last one , regarding QC issue with plotting … SO when doing Array > (pseudo) image plots my RGui in windows complains e.g.: > > If I do: cf <- getFile (cs, 1) > plotImage(cf, transform=list(log2), palette=rainbow > (256)) > > #Loading required package: EBImage > #Loading required package: abind > …. > > I get “Runtime error!” message from Visual C++ and I have to > click 2 times “ok” and then I get the picture… > Here is the link to the error msg:: > http://www.4shared.com/file/209798878/f5a3f82e/Aromaplotimageerror.html > > SO you can imagine I’m not enthusiastic of clicking twice for 300 > arrays and then again for several type of plots. > Any idea where is the issue ? (I guess something with EBImage > dependency make issue ) > Below is my session info . > > Hope you can help . > > Best regards, > > Branko > > -------------------------- > Branislav Misovic, > Department of Toxicogenetics > Leiden University Medical Center > PO.box 9600, Building2,Room:T3-11 > 2300 RC Leiden > The Netherlands > Phone: +31 71 526 9636 > Mob: 0653135855 > E-mail: [email protected] > > > sessionInfo() > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods > base > > other attached packages: > [1] abind_1.1-0 aroma.affymetrix_1.3.4 > aroma.apd_0.1.7 > [4] affxparser_1.18.0 R.huge_0.2.0 > aroma.core_1.3.4 > [7] aroma.light_1.15.1 matrixStats_0.1.8 > R.rsp_0.3.6 > [10] R.filesets_0.6.5 digest_0.4.1 > R.cache_0.2.0 > [13] R.utils_1.2.4 R.oo_1.6.6 > EBImage_3.2.0 > [16] R.methodsS3_1.0.3 > > loaded via a namespace (and not attached): > [1] tools_2.10.0 > > -------------------------- > Branislav Misovic, > Department of Toxicogenetics > Leiden University Medical Center > PO.box 9600, Building2,Room:T3-11 > 2300 RC Leiden > The Netherlands > Phone: +31 71 526 9636 > Mob: 0653135855 > E-mail: [email protected] -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. 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